INSTRUCTIONS FOR RUNNING ON THE CLUSTER


Interactive on hyperion
=======================

ssh -l candler ssh.aem.umn.edu
ssh hyperion-login-2

qrsh -pe orte 240 bash -li
cd /abyss/candler/ERM/
time mpirun --map-by core --bind-to core --mca btl self,sm,openib -np 240 c.out


Submitting to the queue
=======================

#!/bin/bash
#
#$ -pe orte 240
#$ -N trans
#$ -V
#$ -cwd
#$ -S /bin/tcsh

time mpirun --map-by core --bind-to core --mca btl self,sm,openib -np $NSLOTS c.out


Then, run:

qsub -q all.q


Interactive on nike
===================

ssh -l candler ssh.aem.umn.edu
ssh nike-head.nike
cd /abyss/candler/ERM/

Create a machines file (using nike-compute-0-0 to 0-35 and 1-0 to 1-35:

nike-compute-0-1 slots=24
nike-compute-0-3 slots=24
nike-compute-0-4 slots=24
nike-compute-0-6 slots=24
nike-compute-0-9 slots=24
nike-compute-0-10 slots=24
nike-compute-0-11 slots=24
nike-compute-0-12 slots=24
nike-compute-0-13 slots=24
nike-compute-0-14 slots=24

nohup time mpirun -nolocal --mca mtl mx --mca pml cm -np 240 -machinefile machines ./c.out > nohup.out